Successfully complete the game to unlock the EX mode option. This option allows you to play the game again with the money available at the end of your last game, and unlocks new items.

G-Squad mode

Repeatedly fail a mission to unlock the G-Squad mode option, which allows the game to be played on an easier difficulty setting.

Infinite weapons

When you get to the research center on Crimson (the big red place with a lot of "Mutons"). Buy a lot of parts for your weapon and finish the level with them. The next time you return to quest mode you should get the weapon parts you bought in the last mission. You can sell those and get new ones. You can still keep the old weapons if you finished the level with them. The same works for your Neo-Psionics.

Defeating the first Boss

Use your tracking system (press R). Keep shooting until he goes to somewhere else. Shuffle until you track him again and repeat this process until it he is defeated.

Defeating the final Boss

Have at least two Medixir items, the Leviathan 3, and Vulcan 3 barrels. Use L so you can sway from left to right, keeping the monster in your screen. Take the Boss' HP all the way down until he has only a little remaining. Use the Leviathan 3 to do this, then use the Vulcan 3 for the finishing touch. You will probably have to use at least one Medixir before this point. Make sure you do not use the other. Wait until you die to use it. Do not use any Neo-Psionics to fight him; only use Cure 2 and 3 on yourself.